[BioC] GOstat

Hi Naomi,
Naomi Altman wrote:
> I am starting to use GOstat, and there are several things I do not understand.
>> I managed to get output from HyperGTest. I was able to view the
> enriched categories using htmlReport.
>> I would like to try out the graphing methods, but I have not been
> able to figure out the input. In particular, I assume that since I
> have created a GOHyperGResult object, I should use
>> getGoGraph
>> but I have not figured out what goes into the goIds argument. I
> presume it is some type of node identifier, but where do I find it?
The getGoGraph() function wants a GOHyperGParams object, rather than a
GOHyperGResult object. The goIds would then be the GO IDs that you are
interested in, which can be read from the table produced by htmlReport().
Anyway, I can't get getGoGraph() to ouput what I would expect. It
appears to use GOXXCHILDREN to produce the graph, whereas the other
functions in the examples for that (and related) function(s) use
GOXXPARENTS.
To get what I would expect, you can simply use GOGraph(). Say the top
three GO IDs in your table are ("GO:0019219" "GO:0019222" "GO:0006350").
Then you can get a graph by:
grph <- GOGraph(c("GO:0019219" "GO:0019222" "GO:0006350"), GOBPPARENTS)
plot(grph)
HTH,
Jim
>> Thanks for any assistance.
>> Naomi
>>>> Naomi S. Altman 814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics 814-863-7114 (fax)
> Penn State University 814-865-1348 (Statistics)
> University Park, PA 16802-2111
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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